| # | biogem | description | by | cite | version | released | issues | source | build status | 7d | 90d*) | 7d | 90d**) | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| downloads | commits | |||||||||||||
|
|
Bioinformatics library
(...)
|
|
8 months
|
|
|
|||||||||
|
|
Biogem is a software generator for Ruby in bioinformatics
(...)
|
|
4 weeks
|
|
|
|||||||||
|
|
Binder of samtools for Ruby, on the top of ffi
(...)
|
|
5 weeks
|
|
|
|||||||||
|
|
Gff3 parser for big data
(...)
|
|
9 months
|
|
|
|||||||||
|
|
The Ruby ucsc api: accessing the ucsc genome database using Ruby
(...)
|
|
10 weeks
|
|
|
|||||||||
|
|
Webservice client library for intermine data-warehouses
(...)
|
|
4 months
|
|
|
|
|
|||||||
|
This is a development release
(...)
|
|
2 years
|
|
|
|
|
|||||||
|
|
Log4r wrapper with extra features for roles and sane error handling
(...)
|
|
6 weeks
|
|
|
|||||||||
|
|
Library for visualizing genomic regions
(...)
|
|
4 years
|
|
|
|
|
|||||||
|
|
BioRuby assembly plugin
(...)
|
|
16 months
|
|
|
|||||||||
|
|
Genome scaffolding for human beings
(...)
|
|
9 months
|
|
|
|||||||||
|
|
Lightweight Ruby api for ncbi eutils
(...)
|
|
12 months
|
|
|
|||||||||
|
|
Api to ensembl databases
(...)
|
|
17 months
|
|
|
|||||||||
|
|
Very fast blast xml parser and library for big data
(...)
|
|
9 months
|
|
|
|||||||||
|
|
A BioRuby plugin for calculating the isoelectric point and the charge of a protein sequence
(...)
|
|
11 weeks
|
|
|
|||||||||
|
Pipeline to remove contaminations from est libraries
(...)
|
|
5 months
|
|
|
|||||||||
|
|
A tool to classify and manipulate pfemp1 dbl-alpha sequence tags
(...)
|
|
2 months
|
|
|
|||||||||
|
|
Geneexpression illuminahumanannotation
(...)
|
|
16 months
|
|
|
|||||||||
|
|
Ruby binding for bwa mapping software
(...)
|
|
13 months
|
|
|
|||||||||
|
|
A BioRuby plugin: handling genomic interavals and overlaps
(...)
|
|
13 months
|
|
|
|||||||||
|
|
BioRuby plugin for reading and writing nexml (http://nexml.org)
(...)
|
|
1 week
|
|
|
|||||||||
|
|
Running and parsing of the protein transmembrane domain predictor octopus
(...)
|
|
12 months
|
|
|
|||||||||
|
|
Support for multiple sequence alignments (msa)
(...)
|
|
9 weeks
|
|
|
|||||||||
|
|
A plugin that allows you to parse large blast xml output files lazily, reading only what you need
(...)
|
|
11 months
|
|
|
|||||||||
|
|
A fast parser for fastq files
(...)
|
|
3 weeks
|
|
|
|||||||||
|
|
A BioRuby plugin for interaction with the transmembrane predictor tmhmm
(...)
|
|
2 weeks
|
|
|
|||||||||
|
|
Low memory sequence emitters
(...)
|
|
3 months
|
|
|
|||||||||
|
|
A wrapper for the signal peptide prediction algorith signalp
(...)
|
|
6 weeks
|
|
|
|||||||||
|
|
Does high pairwise alignment of sequencing reads with a template
(...)
|
|
2 years
|
|
|
|||||||||
|
|
BioRuby core plugins, most and stable plugins. blastxmlparser, bwa, samtools
(...)
|
|
8 months
|
|
|
|||||||||
|
|
Hello world plugin for the BioRuby (just for fun :-)
(...)
|
|
16 months
|
|
|
|||||||||
|
|
BioRuby plugin for sun grid engine
(...)
|
|
17 months
|
|
|
|||||||||
|
|
Parse affymetrix cel/cdf files
(...)
|
|
5 months
|
|
|
|||||||||
|
|
Implementation of the plasmoap algorithm
(...)
|
|
4 months
|
|
|
|||||||||
|
|
Programmatic interface to the cnls nuclear localisation signal prediction software
(...)
|
|
1 week
|
|
|
|||||||||
|
|
Enables the localisation predictor wolf psort to be run locally
(...)
|
|
4 months
|
|
|
|||||||||
|
|
A method to get the nucleotide sequence of translations done by the emboss bioinformatics package program transeq
(...)
|
|
13 months
|
|
|
|||||||||
|
|
Restriction enzyme dataset
(...)
|
|
8 months
|
|
|
|||||||||
|
|
Digests dna based on restriction enzyme cut patterns
(...)
|
|
8 months
|
|
|
|||||||||
|
|
BioRuby core ext: plugins which require external library or tools so are not pure Ruby plugins
(...)
|
|
8 months
|
|
|
|||||||||
|
|
Biological extensions for the intermine webservice client library
(...)
|
|
9 months
|
|
|
|
|
|||||||
|
|
Meta package for biolinux distribution
(...)
|
|
7 months
|
|
|
|||||||||
|
|
One-line summary of your gem
(...)
|
|
6 months
|
|
|
|||||||||
|
|
Decoding the dbsnp bitfield
(...)
|
|
6 months
|
|
|
|||||||||
|
|
A Ruby api to the ensembl database
(...)
|
|
5 months
|
|
|
|||||||||
|
|
A simple biogem that allows computation of the aliphatic index of a protein
(...)
|
|
3 months
|
|
|
|||||||||
|
|
Hydropathy scale for BioRuby
(...)
|
|
3 months
|
|
|
|||||||||
|
|
Wrapper around the exportpred algorithm for predicting p. falciparum exported proteins
(...)
|
|
4 months
|
|
|
|||||||||
|
|
Next-generation mapping of mutations
(...)
|
|
8 weeks
|
|
|
|||||||||
|
|
(...)
pre
|
|
|
|
|
|
|
|||||||
|
|
Ruby binding for samtools tabix
(...)
new
|
|
1 week
|
|
|
|||||||||
|
|
Bioinformatics triple-store support
(...)
|
|
2 weeks
|
|
|
|||||||||
|
|
Iterate through a samtools pileup file
(...)
new
|
|
2 days
|
|
|
|||||||||
|
|
(...)
pre
|
|
|
|
|
|
|
|||||||
|
|
Bio-gag is a biogem for detecting and correcting a particular type of error that occurs/occurred in particular versions of the iontorrent dna sequencing kit
(...)
new
|
|
2 days
|
|
|
|||||||||
|
|
Enables parsing of hmmer version 3 reports
(...)
new
|
|
1 day
|
|
|
|||||||||
|
|
Parse pfam hmm definition files
(...)
new
|
|
1 day
|
|
|
|||||||||
*) gem downloads (dl total & dl last 90 days) from
rubygems.org
as of
2012-05-19
**) number of commits on GitHub (last 7 days & last 90 days)
**) number of commits on GitHub (last 7 days & last 90 days)
2012-05-18
2012-05-18
2012-05-17
2012-05-17
2012-05-13
2012-05-12
2012-05-09
2012-05-07
2012-05-06
2012-05-06
2012-05-04
2012-05-04
2012-05-03
2012-05-01
2012-05-01
2012-04-27
2012-04-26
2012-04-25
2012-04-21
2012-04-18
2012-04-14
2012-04-10
2012-04-10
2012-04-04
2012-04-02
2012-03-19
2012-03-17